Use \ingroup, \defgroup to get rid of such notes as:
////////////////////////////////////////////////////
// Optional functions that don't have to be provided.
////////////////////////////////////////////////////
or
////////
//Required functions.
////////

vmcore/include/jit_runtime_support_common.h

Add brief description [@file]

Add detailed description (if necessary)

Document functions (where description is missing)

vmcore/include/mon_enter_exit.h

Add brief description [@file]

Add detailed description (if necessary)

Document functions (where description is missing)

vmcore/src/util/linux/include/platform_lowlevel.h

Add brief description [@file]

Add detailed description (if necessary)

Document functions

vmcore/src/util/win/include/platform_lowlevel.h

Add brief description [@file]

Add detailed description (if necessary)

Document functions

vmcore/include/thread_generic.h

Add brief description [@file]

Add detailed description (if necessary)

Document the function

vmcore/include/thread_manager.h

Add brief description [@file]

Add detailed description (if necessary)

Document functions (where description is missing)

vmcore/include/vm_arrays.h

Add brief description [@file]

Add detailed description (if necessary)

Document functions (where description is missing)

vmcore/include/vm_core_types.h

Add brief description [@file]

Add detailed description (if necessary)

Document functions

vmcore/include/vm_strings.h

Add brief description [@file]

Add detailed description (if necessary)

Document functions

Use \ingroup, \defgroup to get rid of such notes as:
//*** Handle versions
//***** New Interface

vmcore/include/vm_threads.h

Add brief description [@file]

Add detailed description (if necessary)

Document functions (where description is missing)

Use appropriate formatting

Would be great if you could find a chance to fix the aforementioned issues.